[Biopython] Get all alignments of a sequence against another
Mary Kindall
mary.kindall at gmail.com
Thu Mar 13 19:57:19 UTC 2014
This is a primitive question but somehow I could not find a solution to it.
I have two sequences 'large' and 'small' as given below.
>large
XXXXXXXXXXXXXXXXXXXGGGTTVTTSSAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBGGGTTLTTSS
>small
GGGTTVTTSS
I need to align the 'small' sequence to the 'large' sequence. Clearly there
are two places where it can be aligned. I need to get indices of both the
locations. I was trying BioPython's "pairwise2.align.globalms" function but
it is only able to align to the second position.
pairwise2.align.globalms(largeStr, smallStr, 2, -1, -1, 0,
penalize_end_gaps=False)
Ans:
[('XXXXXXXXXXXXXXXXXXXGGGTTVTTSSAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBGGGTTLTTSS',
'-----------------------------------------------------------------------------------------GGGTTLTTSS',
20.0,
0,
99)]
Which parameter can I change here or which other pachage/lightweight free
software can compute this?
--
Mary
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